


Loyalties Shaken

by tigereyes45



Category: Star Wars - All Media Types, Star Wars: Rebels, Star Wars: The Clone Wars (2008) - All Media Types
Genre: Clones coming to term, Multi, Some chapters will have dark themes, Some never do, others shall not be too dark
Language: English
Status: In-Progress
Published: 2017-09-13
Updated: 2017-10-08
Packaged: 2018-12-27 15:39:59
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 5
Words: 5,392
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/12084096
Author URL: https://archiveofourown.org/users/tigereyes45/pseuds/tigereyes45
Summary: A story that views the moments within the Clones' and some of the jedi's doubts about their order. We will see the store from many different views, and see moments of vulnerability we may have never seen from these soldiers before. Some may even find love when they learn what loyalty can gain or lose them.





	1. This isn't Right Sir

Captain Rex wasn’t sure what was going on. Ahsoka had been called to be trialed for a crime the council was already convinced she had committed. Rex couldn’t believe it and he knew Anakin didn’t either. Then again the jedi was solemnly silent as they transported Ahsoka to the council. Looking at her in handcuffs made his chest hurt. He was hopeful that the council would come to realize that they had made a mistake.

Then she ran away, refusing to be judged for a crime she didn’t commit. Ahsoka ran away. It made her look more guilty than anything else the council had before. Captain Rex and Anakin chased after her desperately. He did not want one of the other clones to shoot the fugitive before they could apprehend her and bring her back safely. He bit back his tongue as he follows Anakin. He felt like he should say something but if he did it would only interfere with things and they wouldn’t let him lead the search. Rex knew how things like this would play out. He’s seen it before but not often amongst the jedi.

In the end she managed to escape the city. Other clones took the claims that she committed the murder seriously. Rex new better. “Ahsoka would never do something like this.” He had declared and now her wanted poster was everywhere. By all accounts she was guilty. So he hoped she could prove herself innocent. Anakin did not talk much with the clones during this time. He was too busy defending his padawan’s action against the council and chasing her down with the clones. Captain Rex and Commander Wolffe were charged to find her. So the 501st squadron worked with Wolffe’s and hunted the padawan down. She was eventually found and taken in by Plo koon and Skywalker.

Now Rex stood with his men in one of the locker rooms. He had not heard any news of Ahsoka’s fate and Fives was trying to convince him that it would be okay. They would realize Ahsoka wasn’t guilty and then she would be back at it with Anakin and Rex again. They would fight against the separatist and this would all just be a bad memory. Another one they overcame together. Just like when she had fallen to the darkside and was resurrected. Rex shivers as he remembers that little adventure of theirs. It’ll all end well the commander will be proven not guilty and then she would return home to the General and their men. They’ll have their commander and general back and will fall back into the army serving the republic together and completing missions.

Rex didn’t notice that he had left the others until he was standing in front of a very familiar door. The general’s door. Rex considers leaving before he finally decides that there was no way he was going too. He knocks on the door, rapping his knuckles against the metal.

The door slides open and a grim faced Anakin stands on the other side. Rex waits for the general to grant him permission to step inside. Anakin was glaring at his hands lost in thought sitting on his bed against the wall. Rex coughs to gain his attention. The general gives him a confused look.

“General.”

“Come in Rex.” The captain walks into the room straightening his posture as the door closes behind him.

“General,”

“They’re giving her a trial. It’ll only be a matter of time.”

“Shouldn’t we be there?” Rex asks.

“You know why we’re not Rex. You’re a clone, and I’m too close to her to attend and judge without my feelings getting in the way.” It was clear he was repeating something another had told him. It sounded as if General Obi-wan had already talked to him.

They stand there in the quiet. Rex watches as Anakin begins to pace. He occasionally would make a comment about one thing or another. Rex wasn’t sure what else to do but he had to make one thing clear. He could explain to his general how he felt about this whole situation with Ahsoka and the jedi.

“This isn’t right sir.” Rex clenches his fist before relaxing them again. Anakin turns to him with anger in his eyes and Rex braces himself. He wasn’t sure what would happen next but he knew Anakin could be very rash when angry.

“I know that Rex.” Anakin says through gritted teeth.

“If you don’t mind me saying so sir, we should be there to help her.” Captain Rex adds. Anakin stands and shoves past the clone. “Sir?”

“I’m going to help my padawan Rex, and I think I know exactly where to start.” Rex follows Anakin out but stops there. He watches his general as he leaves, disappearing beyond a wall.

Rex, going the opposite way, wanders through the halls again. This time he has a set destination for his feet to reach. He may not be able to do much but he would not remain standing around just to let boredom play with his mind. He rests his palm against one of the blasters at his side. He silently follows Anakin’s lead.


	2. Loyalty Shaken

**Summary for the Chapter:**

> This chapter is based on the episodes of the final season that were never released or fully animated. Within those episodes they find Echo, alive, but terribly mutilated by the separatists. If you have not seen them I recommend you go watch even though they were never fully animated, but nearly completely voiced.
> 
> Echo is saved. He is not sure why things are the way they are now.

Echo was unsure of where he was when he had first woken up. All he saw was the fighting on the citadel. They had to stop that droid. They needed that ship. He went first, Fives would cover him and he had a shield. He would be find. He began repeating the algorithm to help him think, it helped with his nerves. He started running off the numbers when the explosion happened. He had no idea what happened next.

When he woke up he saw that he was not alone. It was not the enemy but Captain Rex. It came rushing back. The captain was only there for a second before he just wasn’t. Echo saw the citadel again, he was running taking point again. “Echo? Echo!” He focuses again on Rex’s voice. He was alive, but he wasn’t on the citadel.

“Captain you came back for me.” Echo was surprised, he thought he had been as good as dead, and then he had seen the layouts of a building. All these details over it, and the projects, and research that were held. It was all available to him. That was when Echo realized he was locked away. If he was going to be held captive, then he was going to do what he did best. He memorized it all. He didn’t know what was happening to him or his body but he wasn’t going to waste this opportunity. Now he was happier than ever that he hadn’t.

“Yeah.” Rex replies. He sets Echo down gently. He didn’t want to hurt him and he couldn’t free him yet. So he was careful with him. Echo felt a mix of emotions. He was angry that he had been kept in that machine for so long, for now he could look at it, and saw what they had done to him. He was sad because of the looks Rex gave him. The captain had a lot of regret held in those eyes. Curiosity. He wanted to know why Rex and Anakin were with a strange batch of clones and why Fives wasn’t with them. Those answers could wait later however. He also felt an overwhelming sense of joy and eagerness as he was set free. Sure there was pain but now he was free and he could help fight again and provide a way out, as well as intel no one else has on the separatist. He could help his brothers escape from this place and deliver a decisive blow to those who had held him captive as part of their machinery.

“Still a show off sir.” Echo says jokingly to Anakin. He was glad to see that some things didn’t change. He hadn’t seen Ahsoka or Fives yet. He couldn’t wait to be back among them all again, even if he was a bit deformed now. Still this would be an advantage in the end. That’s what he kept telling himself as they ran, and fought, and made new allies with the natives. That’s what he kept saying until he finally made it back to their base. Rex had given him to Kix so he could go and get changed. He was so glad to be back in Republic clothing.

“Kix, where’s Fives?” Echo had asked while he was changing. He pauses after slipping on the lower half of his armor. His brother simply coughed into his hand and averted his eyes away from the saved clone. Having watched his brother’s expressions carefully throughout the years that they fought together. He could tell that Fives was gone. His original squad was all gone now, except for him.

“Thank you.” Echo whispers as he shoves his arms through the armor. Once more he felt lonely. Echo, 501st domino squad, the last remaining member.

He had to speak with General Anakin and Captain Rex. Kix argues and tries to stop Echo but the clones pushes ahead anyways. He was quick to find them and immediately realizes that they were already discussing new battle plans and a way to get rid of the separatist main forces. They needed a way to get into the separatist computers to stop the algorithm that they had stolen from him. Of course he was angry, but he knew he had to help them stop the algorithm from transmitting and that he could help. Being angry wouldn’t make the situation better at all.

“Excuse me General. I can help.” Echo looks at the stump of his hand that was covered in separatists machinery.

“Echo you should be,” Captain Rex begins but Echo continues.

“I can hack into their systems.” Echo approaches the hologram table. He takes a deep breath before he inserts his arm into the systems information access that was typically for droids.

He shows off his new abilities, ignoring the pain in his chest that was forming in the back of his head. All the memories of his past, the deaths of his brothers, Fives shouting, darkness, repeat. They kept repeating. He would need a psych evaluation, but he wasn’t going to have one yet. He convinces them to allow him to go on the mission. At first everything was working but then he was spiked. He hadn’t realized the danger of him getting attacked while in the system. A mistake, he should have. They were quick to forgive, Rex and Anakin. Quick to forgive and offer a spot on their team again. He was being welcomed back even though he was now terribly deformed. They cut off the glove part of his suit, for his metal stump. He was determined to make himself useful. Pushing back all thoughts and questions about Fives fate, and everything else that had happened while he was gone. He focuses on his job, his missions, making sure everything goes smoothly, checking and double checking everything once again. Some of the jedi and clones were apprehensive about him being allowed to look at their new battle formations and secret information, but Rex trusted him, General Skywalker trusted him. He was happy to know that to some he was still their brother and friend. Still the thought also causes him much unnecessary pain.

He could hear his brother’s voice, whenever he went back over the plans out loud to hear himself talk. When the nights were dark and he alone was up, busying himself with anything he could. Echo worked tirelessly to make up for all the lost time with his brothers and all the information he had given the separatist. Yet he found it hard to be around them. He would be talking with them and for no reason he would grow angry. The doctor said it was stress. “Stress.” He repeats.

“Echo, look out!” Echo jumps at the voice and quickly reaches for his weapon. However another hand catches his own.

“What are you still doing up soldier?” It was Captain Rex.

Echo tries to lower his arm and Rex lets him go. It falls limply to his side. He looks around once more. That voice he had heard was the same voice as all of theirs, but it sounded like Fives to him. The last thing he had heard Fives say. “Work, sir.” Echo answers. It was impossible. Fives was gone or so the rest had made it seem. Even without Kix vocalizing the loss it was clear and like the soldiers they are, they went back to war. Continuing to fight for the republic, like he should have been doing.

Rex turns his head to look at the systems. Echo wasn’t sure what all the Captain saw when he looks at the machines. Echo himself felt as if he could see all of his brothers and all of their lives when he looks at those machines. They held all their plans, all their strategies, everything that could cost them or pull them through besides their own skills and strength.

“Echo you need to rest.” The captain states.

“I’m fine sir.”

Rex shakes his head. “I wouldn’t define this as fine soldier.”

Echo remains determined. “I’m fine sir.” He repeats.

“What’s going on?” Rex asks his stern face melting away to a look of concern. “Something is clearly keeping you wired.” Captain rex walks over and shuts the maps off as well as the other machines besides the one that were completely necessary.

“Nothing sir.”

Captain Rex shakes his head. He rests his hands down on the messaging system he had stopped next to. He runs a hand over his head and Echo could guess what he would say next.

“Get some rest soldier.”

Echo remains standing in place. The only shift in his stance was when he casts his head to look down at the ground near the Captain’s feet. They stand in silence for a few minutes. Echo knew Rex was waiting for Echo to follow orders or confess what’s wrong. Echo was waiting for the captain to give up and leave him alone. He knew he wouldn’t. Part of him was happy for the Captain’s stubbornness. He really didn’t want to be alone with the ghosts and voices of his brothers who were now gone.

“Sir?”

“Yes soldier?”

“How,  **exactly** , did Fives die?” He puts emphasis on exactly. He had heard whispers. Some of his brothers spat the name out in disgust from their mouths. Others only in hushed whispers. They did the same with Ahsoka. With Tup they at least spoke of his death. A disease of some kind that was in his head. From a planet he had been too. Echo raises his head to look his Captain squarely in his eyes.

“He died in my arms.” Rex answers slowly. The captain tosses his head down and looks away from his brother. “He had been framed for attempting to assassinate chancellor palpatine.” Rex said frame. Does that mean he truly wasn’t guilty? Did the others know? How did Rex know?

“Sir, I,” Echo coughs into his hand. “How?” Rex had said why but not how. Echo felt he needed to know. He had the right to know.

“Commander Fox killed him on orders from the chancellor himself.” Captain Rex squeezes his fists.

Echo finds that his vision was blurry now. He could barely make out the captain in front of him. He feels his body shaking and even the metal on his body reverberating with the rest of him. He falls to his knees and was only partially aware that the captain had now moved closer to him. His whole squad was gone now. His brothers, Fives, was gone. What was the point of fighting for a republic if it just meant that they were all going to die. What was the point of fighting for jedi and politicians who would order their deaths for false crimes. Rex had said he wasn’t guilty, then why did he die? Rex said he wasn’t guilty, how would Rex know.

“He just wanted to do his job as a soldier.” He hears Rex voice from somewhere distant but feels the arms around his head.

“He just want to do his job as a soldier. He just wanted to do his job. He just wanted to be a soldier. A soldier.” Echo repeats. “He was a soldier. A good soldier and a good brother.” He whimpers before asking, “What is the point of a soldier when they die at the hands of their own brothers?”

“I don’t know Echo. I don’t know.” Rex admits. Echo could feel Rex grow tense as he answers and knew that he was trying not to dwell on the hopelessness of it all. Of the point of all their lives.

Echo sits there until the wells of tears in his eyes dry up. When he was tired and could no longer cry or question the injustice of it all he reaches up and rests his hand on Rex’s arm. His metal stub rests lightly against the arm. Rex slowly lets him go and Echo tries to stand up. He falls back and Rex quickly catches him.

“Time to rest Echo.” Captain Rex says once more as he helps the other clone stand upright. Echo felt as if he wasn’t the only one who was repeating himself quite often these days. They walk back to the two large tents where the 501st squadron and their generals rest. Rex let’s Echo walk forward towards the tent. Echo could feel his eyes on the back of him, and maybe that’s what made him pause to say one last thing to the captain. For Echo knew he was not going back to sleep for tonight. Maybe he could think about and solve the problems Echo could not solve in his own mind.

“I’m a soldier Captain. I’ll rest. I’ll wake up and I’ll continue to fight alongside my brothers. That’s my job and I won’t do it with lackluster. Once this is all over, I’ll have nothing else to do. I won’t be a soldier anymore. All that will be left is an echo Captain. The echo of all the brothers we have lost. That’s all any of us will be. Tell me, what are we supposed to do then? This war can't last forever afterall.”

The captain was quiet. Echo took that to mean that he had no answer for him. Echo reaches for the ten flaps to go inside but his hands pauses. He stares down at his metal stump. If it wasn’t for his brothers and General Skywalker he would have never been saved. If it wasn’t for the Republic then he never would have been stuck working for the separatists or even created. He owed his life to the republic and he had never questioned the orders of his superiors except for in the most extreme of situations. Yet he could not help but wonder if what some of his other brothers had said held any truth.

“Captain there must have been a reason Ahsoka left the order, correct?” Echo asks. He looks over his shoulder towards the Captain. “Maybe, maybe there’s a reason for us to leave as well.” He didn’t want to be a slave that would just be thrown away in the end.

“If good soldiers end up like Fives then, maybe we should leave.”

“That’s treason soldier.” Captain Rex says warningly.

“I know.” Echo chuckles. “I know. My mind isn’t right tonight sir. Pardon my words Captain. I forgot my place.” He walks inside and closes the tent flaps behind him. He stumbles over to his makeshift bed and falls into it to rest. It wasn’t long before Echo was asleep and dreaming of the mistakes of his past.


	3. Dead Allies

**Summary for the Chapter:**

> Ahsoka as she feels the great loss of the jedi.

‘I’m safe. Don’t worry.’ Read the message she sent him. She left out the fact that she was stuck on a planet with a sith after her. Ahsoka did not want him to know that or else she would have jedi and clones after her as well. Rex meant well and Ahsoka was happy that the clone promised not to tell the jedi of their correspondence. Something dark was going on within the army and Ahsoka worries for Rex just like Rex worries for her who was stuck outside of the jedi order now and on her own.

Ahsoka would also send Obi-wan messages occasionally, but not as often as Rex. There were times when she felt really brave she would message Anakin. Only she did not do this often, for her master could react in a number of ways. A few times he was monotonous in the way he would talk with her, other occasions he would be happy to see her, and on bad days he would reject her messages and refused to acknowledge her at all.

Obi-wan was often kinder. He never would send voice calls or holo messages away. He always replied to emails even if it often took awhile for him to get around to her. It was hard for her to get ahold of the jedi and for the jedi to reach her as well. That was her ideal situation, she had planned for jedi who would chase her down, however she was not expecting to encounter so many dark force users so soon after leaving the order behind. So she took to the woods of the planet to lose them in.

She had been hiding out in there for a few months. No one was replying to her messages today. Within the last few months Obi-wan, and Anakin, have both remain unresponsive. Only Rex was replying to her nowadays and even those were rare. At the moment Ahsoka was sitting quietly reading over his latest message. Eating some fruit from the tree she had slept in last night. She smiles at the message. The Captain had just made her aware of the recovery of Echo. Rex was concerned about the soldier. Going as far to say that he feared the Generals would have him discharged from the army. Ahsoka understood the situation was dire but how rex wrote so genuinely over the health of their friend. It warmed her inside just a bit.

That was where she was when she felt the great loss. It tears through her and causes her to double over in pain. She felt the tears welling up in her eyes and she tries to fight them back. It couldn’t be true. The life forces she felt fading, they couldn’t be who she thought they were. With a choked sob she clasps her hand around her mouth. She bites down on her hand as the pain grows and she feels the lives disappearing. Joining the force. One death hit her exceptionally hard. She could tell immediately who it was and it made her cry out. Plo Koon was dead. The jedi were disappearing. They were dying. Why?

Ahsoka clenches the ground with her other hand as she tries to make it stop. She had felt lives join the force before but never so many and it had never hurt this much before. Eventually the light on this planet left. In the darkness she lays still the pain beginning to subside. It was so strong and she could feel so many lives that were now just gone. Their loss causing a feeling of emptiness overtaking her every sense.

“No, please no.” She begs as the pain causes her to fall. They were all disappearing. All of them. The order. It’s gone.

“Ahsoka!” She jumps at the sound of her name only to see her fateful Captain firing off a round. “Ahsoka run!” He warns her, and she tries to. She tries to escape the fate she felt befalling upon all of her old allies.

Stuck on the ground her vision of Rex vanishing. She could hear the screams of pain. Strong feelings overpowering her ability to move. It felt as if a hundred of lives were being lost all at the same time. Great betrayal causing the waves to become ten times stronger at her.

Ashoka manages to push herself up against the base of a tree. She writhes in pain and holds a hand over her chest. The other flies towards her lightsaber. She clutches it close to her, prepared to fend off any sort of person or animal who may find and try to harm her in her current weakened state. She suffers there, against the tree, breathing ragged, as her connection with the force tears her apart. Even long after it was done and they were all gone she still felt the pain. The raw emotions that the jedi had never been known for. It was over, they were gone. The jedi were dead. The force had not been enough to protect them. How could it ever be enough to protect herself with?


	4. Chapter 4

**Summary for the Chapter:**

> Boil is left with a haunting feeling as he watches Obi-wan crash into the water. What had they done? He does not know, but he does know he has failed Waxer, and the dear child they had met seemingly so long ago. Poor Numa.

Behind his helmet no one could see his face, but he could see all of them. He watches as Cody guns down Kenobi after giving him his lightsaber back just moments ago. The command had gone out and now the jedi were the enemy, no longer were the droids the ones that held the attention of the clones’ gunfire. He would admit, he shot at Kenobi as well, but he knew his blaster’s shots got no where close to actually hitting the jedi. He wasn’t sure if he was happy about that or not. He wasn’t really sure what was going on here anymore.

Once Kenobi was down they went about cleaning the field and going over the casualties. He was in charge of getting the remaining clones under the commander’s unit back to base. He did so of course and once they were all back when everything was done something in him clicked. What had they just done? At the base, reports were coming in from many teams that their jedi were down.

“Order 66 has been followed sir.” Commander Cody informs someone on the other side of the comm link. There was a raspy “good” from the other side and then the voice was gone.

“Commander?” Boil calls out as Commander Cody takes a datapad from someone else.

“Yes Boil?”

He wanted to say something but he wasn’t quite sure how to get it across. Obi-wan Kenobi was dead that was certain. His body was unretrievable and he was certain the commander would earn a promotion for his deed but something felt off.

“Excuse me sir, but who gave the order?” He asks unsure of how to approach his commander at the moment. He was happy for him but also felt something else. Was it fear? Or something worse….doubt?

“The emperor has deemed all jedi as traitors to the empire, Boil.”

The empire? They were an empire now? Boil nods acceptingly and decides not to push his commander with anymore questions. If the jedi were traitors then they hadn’t been as incorruptible as everyone had thought they were. If even jedi fall who is truly worth following after all. Boil finds a nice spot to sit after the day was over. He puts a bit of distance from himself and the others. He heard some clones cheering, others he could hear sobbing in their tents. Some were just as silent as he. Boil realizes something and wishes dearly that Waxer was still around. Even though another part of him was glad that he wasn’t to be put through this. He stares at his gun and with a sigh of defeat he accepts what they all had done. What he and his brothers had done. “I’m sorry Numa, Waxer. I’m so sorry.” The republic has failed. They were the empire now. His fist clenches around the weapon in his hands and he tries his hardest to stop his shaking body.


	5. Ghost Stories

**Summary for the Chapter:**

> Bly sees Secura again after order 66.

It was late. He should be asleep, but his dreams were violent and sleep remained elusive of him tonight. They were still in those damn jungles. Some of the men thought they would be rescued by now since the war was over. He knew better though. With a sigh he removes his helmet and looks over the scratches on the side. You did not live this long as a clone without learning a few things.

“Bly?” The voice reaches his ears. A ghost whispering names to the back of his mind. No, he would not respond. He would not give her the satisfaction. The ghost would not have its way with him. Not this night.

“Bly? Are you worried?” General Secura asks. Her hand leaving behind a feeling of emptiness on his shoulder.

“No. Not at all, General Secura.”

A laugh, hollow and empty. It casts echoes throughout the cave. “You never say it, but I know there are times when you are worried. I know there are nights where you can not sleep Bly. I know the events you’ve witnessed haunt your dreams.” Her voice was shrill and sent a shiver down his spine. He works to suppress it, not wanting to give that ghost anything it wanted. He would not let it’s icy words change him or his dedication. This was his life. It was his job. He was a soldier by every definition of the word. It was all he has ever known.

“Go away.” He orders the ghost. “You are not real. I know you are not real. You can not be here.”

“Why?” The ghost asks. It slides her arms down his chest. They felt oddly familiar. “Is it because you shot me?” Suddenly the comfort of the scene changes. She is no longer embracing him as she had done before. Instead her arms were now wrapping around his neck, tightening. Her nails dug into his neck as her breath grows chillier. The hair on his neck stands. He reaches up to her hands. He tugs and tugs trying to tear the hands free from his neck.

“You killed me Bly. I trusted you and your men. Our men. My men. You all shot me in the back, and now I’m dead.” Her strength grows as he is sure blood is now dripping from his neck. “You killed me, and you didn’t even look me in the eye.”

“I-i couldn’t.” He tries to explain. He drops his hands, giving up his fight. If she killed him now it would only be because he deserved it.

“Couldn’t or wouldn’t Bly? I never stood a chance.” Aayla sneers.

“I know.” He can barely breathe now. “I know General Secura. I-i’m,”

“Don’t you dare say sorry.” She sneers pushing him forward. In a moment’s breath he was on the floor gasping for air. She was upon him the next hands flying back to his neck. Her blue skin looking luminescent in the night. She was translucent, ghostly, and as breathtaking as ever. “You don’t get to say sorry.” Long, slender, cold fingers sap the warmth from his body as a cold overcomes him.

“You have to live with that fact. Everyday now. For the rest of your short days.” She whispers into his ear as he vision grows black.

With a start Commander Bly wakes up. With a quick glance around he realizes that he was still with his men. They were still in the clearing where they had made camp a few hours after dark. His breathing was ragged and immediately he sought to remedy that. A clear mind was the only sort fit to fight with. So with a few deep breaths to slow down his heart rate Bly checks on his men. In the corner next to him there where Aayla would usually lay, was instead a soldier. Sitting on a long glaring at the fire. In armor he recognized belonged to a dead man.

“Lucky?” Bly asks. In turn the ghost simply points beyond him towards the flames.

The shadows cast by the fire seemingly wrapped their ways around his men, and Bly shook with awareness as he accepted the fact they would all die here. Just as the ghost on the log had past. In the same place where they had cut down their General, they too would die. What had he done?


End file.
